MERFISH Report

1. Overview

Principle Investigator: Mehrdad Shamloo
Institution: Stanford
Project: SPR22-003 Aged Sleep Deprivation study

1.1 Slice Submission

This is the detailed slice information we got from collaborators:

Sample ID	Anatomical source	Preparation method	Treatments	Species & Genetic background	Sex	Age
1	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 18 months	mouse c57bl6	m	18 mo
2	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 18 months	mouse c57bl7	m	18 mo
3	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 18 months	mouse c57bl8	m	18 mo
23	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 18 months	mouse c57bl9	m	18 mo
24	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 18 months	mouse c57bl10	m	18 mo
25	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 18 months	mouse c57bl11	m	18 mo
31	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 4 months	mouse c57bl12	m	4 mo
32	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 4 months	mouse c57bl13	m	4 mo
33	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 4 months	mouse c57bl14	m	4 mo
34	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 4 months	mouse c57bl15	m	4 mo
35	brain hemisphere	perfused and flash frozen in OCT embedding media	No Sleep Deprivation- 4 months	mouse c57bl16	m	4 mo
36	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 4 months	mouse c57bl17	m	4 mo
37	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 4 months	mouse c57bl18	m	4 mo
38	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 4 months	mouse c57bl19	m	4 mo
39	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 4 months	mouse c57bl20	m	4 mo
40	brain hemisphere	perfused and flash frozen in OCT embedding media	Sleep Deprivation- 4 months	mouse c57bl21	m	4 mo

1.2 Sample Information

A brief sample information is generated from the submission table for the following analysis.

“SD” refers to “Sleep Deprivation” while “nSD” refers to “No Sleep Deprivation”.

Sample Index and Basic Information
Batch	Index	Genotype	region	Mice Age (month)	Data Path
1	nSD1	nSD	region_0	18	202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101
1	SD23	SD	region_1	18	202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101
2	nSD2	nSD	region_0	18	202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201
2	SD24	SD	region_1	18	202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201
3	nSD3	nSD	region_0	18	202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201
3	SD25	SD	region_1	18	202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201
4	SD36	SD	region_0	4	202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101
4	nSD31	nSD	region_1	4	202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101
5	SD37	SD	region_0	4	202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101
5	nSD32	nSD	region_1	4	202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101
6	SD38	SD	region_0	4	202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201
6	nSD33	nSD	region_1	4	202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201

1.3 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 5.0 in most area can be considered as a good quality standard.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

2. Data Processing & Analysis

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified ** 712944** cells across 12 samples.

Segmented Cell Count in each Samples
Sample Index	Cell Count
SD36	66786
SD24	65480
nSD31	62351
SD25	60474
SD23	59687
nSD3	58384
nSD2	57578
SD37	57423
nSD32	56953
nSD1	56686
nSD33	56259
SD38	54883

Identified Cell Spatial Overview on all Samples

2.2 Batch Effect & Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.

Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.

Transcript counts on each sample

Umap of cells and colored by batch

Umap of cells on each batch

Leiden Umap can be dividied to 28 clusters

2.3 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)[https://doi.org/10.1016/j.cell.2020.04.007]. Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

2.3.1 Low Resolution Class

MapMyCell Annotation Cell Count (Low resolution class)
class_name	count
31 OPC-Oligo	168524
30 Astro-Epen	112863
33 Vascular	80432
01 IT-ET Glut	79488
09 CNU-LGE GABA	46138
02 NP-CT-L6b Glut	26178
19 MB Glut	23711
20 MB GABA	23531
34 Immune	19905
12 HY GABA	17968
18 TH Glut	16273
27 MY GABA	13050
11 CNU-HYa GABA	12030
10 LSX GABA	9649
07 CTX-MGE GABA	8601
14 HY Glut	8382
23 P Glut	7868
26 P GABA	6320
24 MY Glut	5293
06 CTX-CGE GABA	5004
08 CNU-MGE GABA	4806
05 OB-IMN GABA	4294
13 CNU-HYa Glut	3073
32 OEC	2658
04 DG-IMN Glut	1602
21 MB Dopa	1572
28 CB GABA	1073
03 OB-CR Glut	624
29 CB Glut	529
17 MH-LH Glut	524
22 MB-HB Sero	516
16 HY MM Glut	373
25 Pineal Glut	57
15 HY Gnrh1 Glut	35

2.3.2 High Resolution Class

MapMyCell Annotation Cell Count (High resolution subclass)
	subclass_name	count
7	327 Oligo NN	155504
3	333 Endo NN	51244
11	318 Astro-NT NN	42990
0	319 Astro-TE NN	42944
183	062 STR D2 Gaba	19098
12	334 Microglia NN	17604
31	030 L6 CT CTX Glut	17454
191	061 STR D1 Gaba	16343
24	006 L4/5 IT CTX Glut	15131
8	331 Peri NN	14424
5	321 Astroependymal NN	14038
2	326 OPC NN	13020
219	151 TH Prkcd Grin2c Glut	10526
20	004 L6 IT CTX Glut	9409
17	007 L2/3 IT CTX Glut	8913
146	181 IC Tfap2d Maf Glut	8894
32	005 L5 IT CTX Glut	8516
50	010 IT AON-TT-DP Glut	8110
1	330 VLMC NN	7734
18	009 L2/3 IT PIR-ENTl Glut	6929
195	063 STR D1 Sema5a Gaba	6476
130	323 Ependymal NN	5675
9	332 SMC NN	5206
44	022 L5 ET CTX Glut	5082
60	020 L2/3 IT RSP Glut	4968
26	052 Pvalb Gaba	4876
46	285 MY Lhx1 Gly-Gaba	4508
43	016 CA1-ProS Glut	4380
59	101 ZI Pax6 Gaba	3944
54	029 L6b CTX Glut	3579
42	325 CHOR NN	3337
30	053 Sst Gaba	3146
40	069 LSX Nkx2-1 Gaba	3131
62	032 L5 NP CTX Glut	3123
78	093 RT-ZI Gnb3 Gaba	2933
10	328 OEC NN	2658
38	017 CA3 Glut	2654
204	060 OT D3 Folh1 Gaba	2452
180	235 PG-TRN-LRN Fat2 Glut	2381
69	198 IC Six3 En2 Gaba	2366
131	202 PRT Tcf7l2 Gaba	2338
33	070 LSX Prdm12 Slit2 Gaba	2262
76	098 AHN-SBPV-PVHd Pdrm12 Gaba	2229
21	046 Vip Gaba	2212
29	071 LSX Prdm12 Zeb2 Gaba	2205
107	300 PARN-MDRNd-NTS Gbx2 Gly-Gaba	2160
225	148 AV Col27a1 Glut	2025
72	320 Astro-OLF NN	1987
205	154 PF Fzd5 Glut	1971
135	207 SCs Dmbx1 Gaba	1829
4	329 ABC NN	1824
52	201 PAG-RN Nkx2-2 Otx1 Gaba	1794
141	205 SC-PAG Lef1 Emx2 Gaba	1789
53	041 OB-in Frmd7 Gaba	1778
260	129 VMH Nr5a1 Glut	1776
118	057 NDB-SI-MA-STRv Lhx8 Gaba	1753
167	243 PGRN-PARN-MDRN Hoxb5 Glut	1702
85	306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba	1687
6	049 Lamp5 Gaba	1648
271	104 TU-ARH Otp Six6 Gaba	1634
273	215 SNc-VTA-RAmb Foxa1 Dopa	1572
188	037 DG Glut	1569
108	064 STR-PAL Chst9 Gaba	1415
236	134 PH-ant-LHA Otp Bsx Glut	1351
148	222 PB Evx2 Glut	1343
138	213 SCsg Gabrr2 Gaba	1340
82	304 NTS-PARN Neurod2 Gly-Gaba	1314
77	195 SNr-VTA Pax5 Npas1 Gaba	1278
34	338 Lymphoid NN	1265
73	203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba	1248
152	090 BST-MPN Six3 Nrgn Gaba	1244
13	210 PRT Mecom Gaba	1216
282	102 DMH-LHA Gsx1 Gaba	1182
28	199 PAG-MRN-RN Foxa2 Gaba	1171
105	209 SCs Pax7 Nfia Gaba	1121
222	107 DMH Hmx2 Gaba	1067
99	089 PVR Six3 Sox3 Gaba	1064
192	081 ACB-BST-FS D1 Gaba	1046
264	086 MPO-ADP Lhx8 Gaba	1042
196	088 BST Tac2 Gaba	1024
142	073 MEA-BST Sox6 Gaba	1005
143	068 LSX Otx2 Gaba	1004
215	106 PVpo-VMPO-MPN Hmx2 Gaba	996
209	182 CUN-PPN Evx2 Meis2 Glut	996
229	217 PB Lmx1a Glut	987
74	200 PAG-ND-PCG Onecut1 Gaba	981
137	187 SCsg Pde5a Glut	959
171	176 SCig Foxb1 Glut	955
93	002 IT EP-CLA Glut	926
47	045 OB-STR-CTX Inh IMN	922
23	047 Sncg Gaba	919
102	056 Sst Chodl Gaba	909
147	119 SI-MA-LPO-LHA Skor1 Glut	895
90	264 PRNc Otp Gly-Gaba	894
70	322 Tanycyte NN	893
56	251 NTS Dbh Glut	865
144	085 SI-MPO-LPO Lhx8 Gaba	864
79	317 Astro-CB NN	860
139	208 SC Lef1 Otx2 Gaba	857
217	168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut	854
155	177 SCig-an-PPT Foxb1 Glut	850
88	076 MEA-BST Lhx6 Nfib Gaba	848
216	100 AHN Onecut3 Gaba	837
227	224 PCG-PRNr Vsx2 Nkx6-1 Glut	830
66	033 NP SUB Glut	826
110	054 STR Prox1 Lhx6 Gaba	825
169	180 SCiw Pitx2 Glut	824
226	164 APN C1ql4 Glut	812
124	147 AD Serpinb7 Glut	774
207	173 PAG Pou4f2 Glut	773
101	039 OB Meis2 Thsd7b Gaba	769
91	221 LDT-PCG Vsx2 Lhx4 Glut	747
133	212 SCs Lef1 Gli3 Gaba	746
116	103 PVHd-DMH Lhx6 Gaba	744
114	025 CA2-FC-IG Glut	742
81	267 CS-PRNr-PCG Tmem163 Otp Gaba	739
87	021 L4 RSP-ACA Glut	728
157	172 PAG Pou4f1 Ebf2 Glut	722
281	074 MEA-BST Lhx6 Sp9 Gaba	721
193	058 PAL-STR Gaba-Chol	721
250	132 AHN-RCH-LHA Otp Fezf1 Glut	706
194	079 CEA-BST Six3 Cyp26b1 Gaba	702
14	337 DC NN	677
182	278 NLL Gata3 Gly-Gaba	670
159	162 CUN Evx2 Lhx2 Glut	655
92	072 LSX Sall3 Lmo1 Gaba	655
49	283 PRP Otp Gly-Gaba	642
249	108 ARH-PVp Tbx3 Gaba	639
104	196 PAG-PPN Pax5 Sox21 Gaba	638
96	265 PB Sst Gly-Gaba	625
267	082 CEA-BST Ebf1 Pdyn Gaba	611
22	192 PPN-CUN-PCG Otp En1 Gaba	604
198	055 STR Lhx8 Gaba	598
83	270 LDT-DTN Gata3 Nfix Gaba	591
75	023 SUB-ProS Glut	583
165	238 NTS Phox2b Glut	574
95	027 L6b EPd Glut	568
311	128 VMH Fezf1 Glut	557
36	305 SPVI-SPVC Sall3 Nfib Gly-Gaba	551
224	163 APN C1ql2 Glut	544
223	150 CM-IAD-CL-PCN Sema5b Glut	543
181	175 SC Bnc2 Glut	538
154	169 PAG-SC Pou4f1 Zic1 Glut	531
48	003 L5/6 IT TPE-ENT Glut	520
235	216 MB-MY Tph2 Glut-Sero	516
51	277 DTN-LDT-IPN Otp Pax3 Gaba	515
201	161 PAG Pou4f3 Glut	507
27	019 L2/3 IT PPP Glut	490
203	268 CS-PRNr-DR En1 Sox2 Gaba	485
239	080 CEA-AAA-BST Six3 Sp9 Gaba	485
261	124 MPN-MPO-PVpo Hmx2 Glut	478
160	174 PAG Pou4f2 Mesi2 Glut	476
248	133 PVH-SO-PVa Otp Glut	471
240	094 SCH Six6 Cdc14a Gaba	461
149	146 LH Pou4f1 Sox1 Glut	446
120	035 OB Eomes Ms4a15 Glut	424
156	170 PAG-MRN Tfap2b Glut	418
258	311 CBX MLI Megf11 Gaba	414
125	042 OB-out Frmd7 Gaba	405
35	028 L6b/CT ENT Glut	403
128	197 SNr Six3 Gaba	402
158	171 PAG Pou4f1 Bnc2 Glut	399
202	067 LSX Sall3 Pax6 Gaba	392
136	211 SC Tnnt1 Gli3 Gaba	384
134	139 PH-LHA Foxb1 Glut	380
212	166 MRN Pou3f1 C1ql4 Glut	379
305	136 PMv-TMv Pitx2 Glut	375
161	167 PRC-PAG Tcf7l2 Irx2 Glut	375
283	135 STN-PSTN Pitx2 Glut	367
61	194 MRN-VTN-PPN Pax5 Cdh23 Gaba	363
16	263 CS-RPO Meis2 Gaba	359
173	206 SCm-PAG Cdh23 Gaba	355
151	083 CEA-BST Rai14 Pdyn Crh Gaba	354
19	018 L2 IT PPP-APr Glut	352
163	160 PAG-SC Neurod2 Meis2 Glut	351
279	111 TRS-BAC Sln Glut	344
71	299 MARN-PPY Ngfr Gly-Gaba	341
15	271 NI-RPO Gata3 Nr4a2 Gaba	338
295	117 LHA Barhl2 Glut	333
213	193 MRN-PPN-CUN Pax8 Gaba	331
132	066 NDB-SI-ant Prdm12 Gaba	326
244	110 BST-po Iigp1 Glut	320
140	246 CU-ECU-SPVI Foxb1 Glut	320
247	141 PH-SUM Foxa1 Glut	319
127	254 VCO Mafa Meis2 Glut	319
208	144 MM Foxb1 Glut	316
106	051 Pvalb chandelier Gaba	306
164	245 SPVI-SPVC Tlx3 Ebf3 Glut	306
129	087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba	302
64	272 LDT-PCG-CS Gata3 Lhx1 Gaba	302
175	188 SCop Sln Glut	296
231	165 PAG-MRN Pou3f1 Glut	290
189	013 COAp Grxcr2 Glut	284
200	092 TMv-PMv Tbx3 Hist-Gaba	283
55	314 CB Granule Glut	280
179	140 PMd-LHA Foxb1 Glut	280
199	126 ARH-PVp Tbx3 Glut	276
296	097 PVHd-SBPV Six3 Prox1 Gaba	275
25	050 Lamp5 Lhx6 Gaba	273
57	229 PB-NTS Phox2b Ebf3 Lmx1b Glut	270
109	012 MEA Slc17a7 Glut	268
252	115 MS-SF Bsx Glut	264
115	335 BAM NN	258
100	315 DCO UBC Glut	249
303	125 DMH Hmx2 Glut	248
103	044 OB Dopa-Gaba	246
170	220 PB Pax5 Glut	245
302	127 DMH-LHA Vgll2 Glut	244
277	155 PRC-PAG Pax6 Glut	242
245	152 RE-Xi Nox4 Glut	238
98	313 CBX Purkinje Gaba	237
185	099 SBPV-PVa Six6 Satb2 Gaba	235
293	131 LHA-AHN-PVH Otp Trh Glut	230
232	287 MV-SPIV-PRP Dmbx1 Gly-Gaba	228
290	118 ADP-MPO Trp73 Glut	227
122	048 RHP-COA Ndnf Gaba	225
176	105 TMd-DMH Foxd2 Gaba	223
162	237 PRP-NI-PRNc-GRN Otp Glut	212
197	225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut	209
174	279 PSV Pax2 Gly-Gaba	205
187	114 COAa-PAA-MEA Barhl2 Glut	204
119	290 MY Prox1 Lmo7 Gly-Gaba	203
126	036 HPF CR Glut	200
177	261 HB Calcb Chol	197
238	109 LGv-ZI Otx2 Gaba	197
270	231 IPN-LDT Vsx2 Nkx6-1 Glut	189
145	257 SPVC Ccdc172 Glut	188
246	156 MB-ant-ve Dmrta2 Glut	184
41	293 PAS-MV Ebf2 Gly-Gaba	184
58	308 DCO Il22 Gly-Gaba	182
113	059 GPe-SI Sox6 Cyp26b1 Gaba	181
269	248 MV-SPIV Zic4 Neurod2 Glut	179
45	065 IA Mgp Gaba	173
287	223 B-PB Nr4a2 Glut	172
84	214 IPN Otp Crisp1 Gaba	166
326	292 MV Nkx6-1 Gly-Gaba	165
298	276 LDT-PCG St18 Gaba	164
39	008 L2/3 IT ENT Glut	157
166	149 PVT-PT Ntrk1 Glut	148
67	204 SC Otx2 Gcnt4 Gaba	145
309	116 AVPV-MEPO-SFO Tbr1 Glut	140
153	303 IRN Dmbx1 Pax2 Gly-Gaba	138
172	186 SCop Pou4f2 Neurod2 Glut	136
63	273 PDTg-PCG Pax6 Gaba	130
186	228 PSV Pvalb Lhx2 Glut	130
285	294 MV Pax6 Gly-Gaba	127
168	178 SCig Foxb1 Otx2 Glut	125
297	130 LHA Pmch Glut	124
117	034 NP PPP Glut	123
86	043 OB-mi Frmd7 Gaba	118
286	282 POR Spp1 Gly-Gaba	117
265	288 MDRN Hoxb5 Ebf2 Gly-Gaba	116
254	179 SCdg-PAG Tfap2b Glut	114
278	284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba	114
259	316 Bergmann NN	113
292	084 BST-SI-AAA Six3 Slc22a3 Gaba	113
230	298 PRP Gata3 Slc6a5 Gly-Gaba	112
294	121 MEA-BST Otp Zic2 Glut	111
210	309 CB PLI Gly-Gaba	110
221	113 MEA-COA-BMA Ccdc42 Glut	109
228	233 NLL-SOC Spp1 Glut	108
184	296 RPA Pax6 Hoxb5 Gly-Gaba	108
178	185 SCig Tfap2b Chrnb3 Glut	103
262	159 IF-RL-CLI-PAG Foxa1 Glut	102
68	031 CT SUB Glut	102
220	226 PRNc-PARN Tlx1 Glut	102
65	336 Monocytes NN	101
251	078 SI-MA-ACB Ebf1 Bnc2 Gaba	100
313	312 CBX MLI Cdh22 Gaba	100
214	247 MV-SPIV Phox2b Ebf3 Lbx1 Glut	99
233	234 MEV Ppp1r1c Glut	96
111	075 MEA-BST Lhx6 Nr2e1 Gaba	95
37	014 LA-BLA-BMA-PA Glut	95
256	138 PH Pitx2 Glut	95
94	011 L2 IT ENT-po Glut	93
234	286 PPY-PGRNl Vip Glyc-Gaba	90
268	077 CEA-BST Gal Avp Gaba	84
206	157 RN Spp1 Glut	82
315	145 MH Tac2 Glut	78
263	281 POR Gata3 Gly-Gaba	74
211	123 DMH Nkx2-4 Glut	73
314	297 CU-ECU Pax2 Gly-Gaba	71
266	191 PAG-MRN Rln3 Gaba	69
317	232 LDT Vsx2 Nkx6-1 Nfib Glut	68
80	001 CLA-EPd-CTX Car3 Glut	68
237	291 NTS-MDRNd Prox1 Zic1 Gly-Gaba	67
308	122 LHA-MEA Otp Glut	65
253	256 SPVC Mafa Glut	65
310	252 DMX VII Tbx20 Chol	63
190	015 ENTmv-PA-COAp Glut	61
112	302 MV Xdh Gly-Gaba	60
306	143 MM-ant Foxb1 Glut	57
243	262 Pineal Crx Glut	57
97	040 OB Trdn Gaba	56
257	158 MRN-PAG Nkx6-1 Glut	54
307	230 PRNr Otp Nfib Glut	53
150	153 MG-POL-SGN Nts Glut	48
280	091 ARH-PVi Six6 Dopa-Gaba	47
323	269 LDT Fgf7 Gaba	47
218	190 ND-INC Foxd2 Glut	45
241	275 PDTg Otp Olig3 Gaba	42
274	250 CBN Neurod2 Pvalb Glut	39
334	253 IO Fgl2 Glut	38
332	112 GPi Tbr1 Cngb3 Gaba-Glut	37
291	142 HY Gnrh1 Glut	35
242	038 DG-PIR Ex IMN	33
321	137 PH-an Pitx2 Glut	32
316	244 MV-SPIV Slc6a2 Glut	32
330	096 PVHd Gsc Gaba	31
304	310 CBX Golgi Gly-Gaba	30
319	324 Hypendymal NN	26
301	184 PAG Tcf24 Glut	26
123	307 RO-RPA Pkd2l1 Gaba	25
300	120 MEA Otp Foxp2 Glut	24
288	026 NLOT Rho Glut	23
276	255 SPVO Mafa Meis2 Glut	20
299	218 PSV Lmx1a Trpv6 Glut	19
327	239 MARN-GRN Pyy Glut	19
275	295 CBN Dmbx1 Gaba	19
329	236 IRN Vip Glut	16
272	258 SPVC Nmu Glut	13
255	289 MDRNd Prox1 Pax6 Gly-Gaba	13
324	274 PDTg Otp Shroom3 Gaba	12
322	242 PGRNd Dmbx1 Glut	12
289	095 DMH Prdm13 Gaba	11
333	266 PRNc Prox1 Brs3 Gly-Gaba	9
318	227 PB-PSV Phox2b Glut	8
312	301 MV Nr4a2 Gly-Gaba	7
284	219 PB-SUT Tlx3 Lhx2 Glut	7
331	240 MDRNv Lhx4 Qrfprl Glut	7
89	024 L5 PPP Glut	6
328	249 NTS Aldh1a2 Glut	6
325	189 PAG Ucn Glut	3
320	260 MDRNv Crp Glut	2
121	280 NLL-po Pax7 Gaba	2
335	183 PBG Mtnr1a Glut-Chol	1

2.3.3 Selected Cell Class

Selected Cell Count (Customed subclass)
	select_class_name	count
1	Astrocyte	96912
2	Endo	50134
9	L6b Glut	21511
5	L2/3 Glut	20604
3	Microglia	17253
10	L5 Glut	16403
19	TH Glut	15993
8	L4/5 Glut	14734
11	MY GABA	12482
7	L6 Glut	9129
14	P Glut	7729
4	P GABA	6187
18	MY Glut	5163
17	CA1 Glut	4268
12	CA3 Glut	2579
20	DG Glut	1548
16	CA2 Glut	717
15	L4 Glut	698
13	L5/6 Glut	505
6	L2 Glut	438

2.3.4 Selected Cell Type Umap

2.3.4 Selected Cell Type Spatial Map

2.3.5 Selected Cell Type Proportion

3. Manual Region Selection

Manual selection mostly based on the cell type annotation.

3.1 Hippocampus

3.2 Frontal Cortex

3.3 Locus ceruleus (Unfinished!)

To find LC region, we tries to show LC marker gene expression: Th, Dbh.

Th Gene Spatial Map

Dbh Gene Spatial Map

4. Gene differentiation

Here, we use pseudo-bulk and DESeq2 to compute gene differential expression. The statistical significance was cut-off by log2(Fold Change) > 1 or log2(Fold Change) < -1 and p_value < 0.05.

We also highlight the adrenergic related gene that found in NCBI database.

4.1 Adrenergic Related Gene

Before gene differentiation. We can start with searching potential target genes. Via NCBI Gene Database, we search for adrenergic related genes and subsequently compared them with the MERFISH gene panel. This resulted in the detection of 43 overlapping genes, which we consider as adrenergic related and will be highlighted in gene differentiation analyses.

Adrenergic Related Gene List
Gene
Nrg1
Mki67
Drd5
Agtr1a
Nos1
Pomc
Nos3
Erbb2
Tnf
Cck
Cd14
Fos
Creb1
Agt
Drd2
Sorl1
Il1b
Trpm4
Adora2a
Adam10
Mapt
Tac1
Kcnq1
Cxcr4
Dlg4
Npy
App
Drd1
Cnr1
Rapgef3
Spp1
Mtor
Prkce
Gria1
Th
Adrb1
Bdnf
Snca
Egln3
Gpr55
Ccn2
Gja1
Mapk1
Dbh

4.2 Hippocampus Region

4.2.1 Hippocampus, 4m, SD vs nSD

##            baseMean log2FoldChange     lfcSE       stat       pvalue
## Slc6a3    1364.9733       3.426921 1.0608331   3.230405 1.236148e-03
## Adora2a   4862.6254      -3.351775 0.3519800  -9.522628 1.688538e-21
## Ppp1r1b  27366.2013      -3.300389 0.3037854 -10.864212 1.706912e-27
## Six3      2598.3987      -2.989373 0.4616998  -6.474710 9.499396e-11
## Th        3121.3955       2.903303 1.1774378   2.465780 1.367151e-02
## Penk     13809.5894      -2.737112 0.2842345  -9.629770 5.986357e-22
## Clic6     2858.5186      -2.671303 0.9943850  -2.686387 7.222931e-03
## Col6a1   15572.4225      -2.581616 0.8902951  -2.899731 3.734828e-03
## Pdyn      1785.1284      -2.578127 0.3627920  -7.106350 1.191520e-12
## Drd1      2654.5030      -2.556341 0.3079737  -8.300517 1.036590e-16
## Ccdc153   1152.1289      -2.430435 0.9757703  -2.490786 1.274609e-02
## Agt      12179.6525       1.955604 0.4041071   4.839322 1.302826e-06
## C3         823.6469      -1.847138 0.6055476  -3.050360 2.285672e-03
## Dlx2      1389.3752      -1.834641 0.3734112  -4.913193 8.960503e-07
## Nxph4     1215.3648       1.815283 0.3628801   5.002432 5.661141e-07
## Drd2      2127.2297      -1.802835 0.3928696  -4.588888 4.456129e-06
## Car12     2386.4167      -1.693730 0.4409146  -3.841401 1.223340e-04
## Syt6      5383.2729      -1.664975 0.3394866  -4.904391 9.371765e-07
## Meis2     4755.4902      -1.586100 0.3181207  -4.985844 6.169181e-07
## Syndig1l  5410.1288      -1.567867 0.3873430  -4.047750 5.171239e-05
## Tac1       791.5129      -1.537814 0.2851293  -5.393391 6.914011e-08
## Chrm4     3350.4567      -1.485698 0.3829944  -3.879164 1.048161e-04
## Folr1      534.5439      -1.427654 0.4954915  -2.881289 3.960527e-03
## Cpne5     3512.1566      -1.402412 0.3811532  -3.679391 2.337913e-04
## Dclk3    15621.4163      -1.328636 0.2701100  -4.918869 8.704560e-07
## Npas1     2269.9177       1.291786 0.3929731   3.287212 1.011847e-03
## Sncg      1409.8866       1.265045 0.2997710   4.220038 2.442607e-05
## Scn4b    10629.0169      -1.245762 0.2326462  -5.354750 8.567492e-08
## Lhx6      1508.6415      -1.214062 0.3464598  -3.504193 4.579936e-04
## Fosb      1425.5005      -1.213112 0.4931950  -2.459701 1.390528e-02
## Calb2     4308.3281       1.130460 0.3453881   3.273013 1.064075e-03
## Gpr83     1117.1038      -1.122101 0.3762036  -2.982695 2.857224e-03
## Egr4      1225.2874      -1.108319 0.4230891  -2.619588 8.803608e-03
## Fibcd1    4154.3541       1.021081 0.3070405   3.325558 8.824170e-04
##                  padj
## Slc6a3   2.060247e-02
## Adora2a  2.814230e-19
## Ppp1r1b  8.534562e-25
## Six3     7.916163e-09
## Th       1.287526e-01
## Penk     1.496589e-19
## Clic6    8.025479e-02
## Col6a1   5.187261e-02
## Pdyn     1.191520e-10
## Drd1     1.295737e-14
## Ccdc153  1.225585e-01
## Agt      4.652949e-05
## C3       3.571362e-02
## Dlx2     3.604525e-05
## Nxph4    3.084590e-05
## Drd2     1.485376e-04
## Car12    2.912714e-03
## Syt6     3.604525e-05
## Meis2    3.084590e-05
## Syndig1l 1.436455e-03
## Tac1     4.938579e-06
## Chrm4    2.620403e-03
## Folr1    5.352063e-02
## Cpne5    4.870653e-03
## Dclk3    3.604525e-05
## Npas1    1.806870e-02
## Sncg     7.184137e-04
## Scn4b    5.354682e-06
## Lhx6     8.807569e-03
## Fosb     1.287526e-01
## Calb2    1.834611e-02
## Gpr83    4.081749e-02
## Egr4     9.365540e-02
## Fibcd1   1.634106e-02

4.2.2 Hippocampus, 4m, SD vs nSD

##    baseMean log2FoldChange     lfcSE     stat      pvalue      padj
## Th 444.3555       1.218214 0.3923819 3.104665 0.001904947 0.9486635

4.2.3 Hippocampus, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Th       3052.3640       3.295128 1.2070304  2.729946 6.334464e-03 0.0564445969
## Slc6a3   1410.1921       3.031186 1.0954631  2.767037 5.656841e-03 0.0532596878
## Clic6    2843.6548      -2.652370 1.0472127 -2.532790 1.131586e-02 0.0842778202
## Mapk1    1646.6096      -2.601200 0.5346434 -4.865299 1.142840e-06 0.0004100324
## Folr1     842.4595      -2.256637 0.4850865 -4.652030 3.286833e-06 0.0004100324
## Htr2c    1065.0025      -2.006609 0.4868787 -4.121375 3.766183e-05 0.0023491568
## Ppp1r1b 11668.3012      -1.847722 0.9266973 -1.993879 4.616532e-02 0.2094226917
## Coch      607.6535      -1.662861 0.4105028 -4.050791 5.104478e-05 0.0026016784
## Car12    2326.7882      -1.633785 0.4519679 -3.614824 3.005514e-04 0.0083319525
## Synpr     300.0868      -1.617818 0.4065541 -3.979343 6.910605e-05 0.0028736600
## Rims1    2134.3668      -1.607618 0.3527274 -4.557678 5.172227e-06 0.0005161883
## Pten      764.4947      -1.495198 0.4591520 -3.256435 1.128209e-03 0.0194129719
## Enpp2   18609.8516      -1.480111 0.3178592 -4.656499 3.216324e-06 0.0004100324
## Aph1b     329.6147      -1.475409 0.4198520 -3.514118 4.412171e-04 0.0104841596
## Six3     1102.9927      -1.470478 0.3484817 -4.219669 2.446609e-05 0.0017440827
## Crebbp    761.6576      -1.448981 0.4694416 -3.086606 2.024559e-03 0.0323601810
## Cdh9      698.2533      -1.438795 0.3270097 -4.399854 1.083238e-05 0.0009008925
## Drd1     1431.4307      -1.425556 0.4798458 -2.970862 2.969651e-03 0.0389962098
## Penk     6653.8594      -1.418103 0.7007292 -2.023754 4.299551e-02 0.2043310386
## Cd63      533.2938      -1.402621 0.3634884 -3.858777 1.139558e-04 0.0037000153
## Nrn1     3057.5798      -1.388018 0.2931926 -4.734153 2.199722e-06 0.0004100324
## Ccdc153   648.7175      -1.363386 0.4906130 -2.778943 5.453604e-03 0.0523336258
## Scimp     819.8027      -1.331683 0.3309819 -4.023432 5.735620e-05 0.0026018858
## Enpp6     368.9844      -1.310251 0.3238521 -4.045831 5.213784e-05 0.0026016784
## Npy1r     826.0087      -1.280637 0.3295594 -3.885906 1.019489e-04 0.0037000153
## Gm14964   673.3834      -1.252375 0.3754005 -3.336105 8.496121e-04 0.0157020901
## Gpr37    3649.2234      -1.224901 0.3515209 -3.484574 4.929207e-04 0.0106942350
## Cd2ap    1345.4934      -1.180886 0.4410368 -2.677524 7.416863e-03 0.0610002285
## Tnik      688.3765      -1.179340 0.4184830 -2.818132 4.830389e-03 0.0482072797
## Kctd4    1780.9795      -1.171516 0.3202757 -3.657837 2.543528e-04 0.0074660017
## Nectin3   674.0201      -1.162438 0.4570742 -2.543215 1.098377e-02 0.0830439518
## Gng2     1847.0245      -1.159588 0.4114552 -2.818259 4.828481e-03 0.0482072797
## Tac1      646.8013      -1.117581 0.4106281 -2.721637 6.495941e-03 0.0568679790
## Pdyn      816.2053      -1.116282 0.3284513 -3.398621 6.772652e-04 0.0140814728
## Kcnh7    1099.7148      -1.113718 0.3777099 -2.948606 3.192106e-03 0.0394160686
## Mas1     2100.2391      -1.093538 0.2841153 -3.848924 1.186378e-04 0.0037000153
## Cxcl10    235.2083       1.090587 0.3083791  3.536514 4.054450e-04 0.0101158539
## Fmo1      376.0314      -1.075141 0.3814375 -2.818656 4.822522e-03 0.0482072797
## Creb1     460.1756      -1.051940 0.3569655 -2.946897 3.209802e-03 0.0394160686
## Bace1    1377.1077      -1.037258 0.3245718 -3.195774 1.394565e-03 0.0231962646
## Ace      3182.8865      -1.036258 0.3587287 -2.888695 3.868442e-03 0.0432707008

4.2.4 Hippocampus, nSD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Mapk1    1669.5639      -2.115931 0.7236660 -2.923905 3.456704e-03 0.0711093330
## Dlk1     1041.1257       2.071091 0.6164024  3.359966 7.795217e-04 0.0224502236
## Col6a1  19031.1594       1.760535 0.5218296  3.373774 7.414516e-04 0.0224502236
## Folr1    1832.4643      -1.709645 0.7620983 -2.243339 2.487498e-02 0.1733224198
## Th        538.3247       1.609919 0.3157554  5.098626 3.421274e-07 0.0001186777
## Synpr     318.4506      -1.486967 0.5361688 -2.773320 5.548758e-03           NA
## Synpo2   2752.3557       1.475591 0.6481139  2.276746 2.280137e-02 0.1716919266
## Htr2c    1130.0513      -1.473991 0.5587192 -2.638162 8.335682e-03 0.0999448930
## Crebbp    912.6200      -1.379936 0.5838201 -2.363632 1.809677e-02 0.1563561073
## Six3     3526.4818       1.367953 0.6393661  2.139546 3.239151e-02 0.1967242669
## Penk    18379.6041       1.359137 0.5305433  2.561783 1.041364e-02 0.1071117644
## Rims1    2200.4093      -1.342497 0.4946906 -2.713811 6.651411e-03 0.0957803213
## Dcn       844.5796      -1.286658 0.2845329 -4.522000 6.125812e-06 0.0005292701
## Dclk3   17352.4896       1.285261 0.4294304  2.992944 2.763009e-03 0.0596809860
## Gpr37    3190.4456      -1.283460 0.2562720 -5.008193 5.494339e-07 0.0001186777
## Acta2    1841.9538      -1.281820 0.4017026 -3.190969 1.417967e-03 0.0334730292
## Ddit4l    262.8605      -1.259404 0.4957763 -2.540267 1.107679e-02           NA
## Nectin3   798.3678      -1.248818 0.5164259 -2.418195 1.559773e-02 0.1405763749
## Cldn11  21811.2036      -1.245550 0.2561561 -4.862464 1.159336e-06 0.0001334128
## Adora2a  6936.5057       1.244071 0.6279937  1.981025 4.758851e-02 0.2355246313
## Igf2     7577.2872      -1.237929 0.6089652 -2.032841 4.206862e-02 0.2226103804
## Pdyn     2404.9656       1.224516 0.4406717  2.778749 5.456867e-03 0.0900876939
## Nrn1     3108.9032      -1.189883 0.4481541 -2.655075 7.929066e-03 0.0990135707
## Opalin   2716.5036      -1.166851 0.3018913 -3.865135 1.110277e-04 0.0059954941
## Tacr3     382.8694      -1.122741 0.5412695 -2.074274 3.805388e-02           NA
## Col11a1  2472.6758      -1.119806 0.4266917 -2.624392 8.680380e-03 0.0999448930
## Mog      8346.7775      -1.110528 0.2751478 -4.036112 5.434417e-05 0.0034383397
## Enpp2   20320.3993      -1.080720 0.4717670 -2.290792 2.197547e-02 0.1716919266
## Adarb2    729.0932      -1.039995 0.4698901 -2.213272 2.687887e-02 0.1786411276
## Fibcd1   4600.2944      -1.033393 0.2740133 -3.771324 1.623838e-04 0.0070149784
## Ccn2     1020.3759      -1.027369 0.3875189 -2.651145 8.021933e-03 0.0990135707
## Dlx2     1783.1703       1.023830 0.4607517  2.222085 2.627754e-02 0.1773733750
## Grin3a   1973.2670      -1.009012 0.4726768 -2.134677 3.278738e-02 0.1967242669
## Cd9      2190.5569      -1.000183 0.4423899 -2.260863 2.376773e-02 0.1716919266

4.3 Front Cortex Region

4.3.1 Front Cortex, 4m, SD vs nSD

##         baseMean log2FoldChange     lfcSE     stat     pvalue      padj
## Synpo2  5253.975       1.294972 0.5329267 2.429926 0.01510193 0.9945726
## Tcf7l2 10334.890       1.267829 0.5921721 2.140981 0.03227555 0.9945726
## Clic6   3319.993       1.066931 0.5031460 2.120520 0.03396220 0.9945726

4.3.2 Front Cortex, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE     stat       pvalue      padj
## Dlk1   3535.329       2.697496 1.3066625 2.064417 0.0389782411 0.9976486
## Ngb    2151.579       1.313891 0.6156327 2.134212 0.0328254208 0.9976486
## Calb2 10668.088       1.119273 0.3264835 3.428267 0.0006074466 0.1512542
## Ntng1  5548.844       1.045397 0.4528420 2.308525 0.0209699630 0.9976486

4.3.3 Front Cortex, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue        padj
## Mapk1    6255.2112      -2.513942 0.6472833 -3.883836 1.028214e-04 0.007659816
## Tnik     3185.3111      -1.665473 0.5598671 -2.974764 2.932142e-03 0.099762892
## Rims1    9884.3332      -1.653063 0.3675999 -4.496908 6.894888e-06 0.003447444
## Pten     3267.0055      -1.511649 0.5333828 -2.834078 4.595807e-03 0.135170786
## Crebbp   3116.4107      -1.473675 0.5455952 -2.701041 6.912289e-03 0.168269073
## Synpr     961.8203      -1.423123 0.4312627 -3.299899 9.671961e-04 0.048359807
## Npy1r    3110.9271      -1.415869 0.3545175 -3.993790 6.502543e-05 0.007659816
## Mas1     5805.0479      -1.355472 0.3499252 -3.873604 1.072374e-04 0.007659816
## Nrn1     8807.3603      -1.330843 0.3182181 -4.182174 2.887349e-05 0.007218373
## Kcnh7    5856.3683      -1.316154 0.4287390 -3.069826 2.141835e-03 0.089243134
## Htr2c    2574.0793      -1.309623 0.6199822 -2.112355 3.465599e-02 0.320275211
## Coch     3242.5834      -1.308947 0.3592633 -3.643420 2.690397e-04 0.016814980
## Aph1b    1362.3544      -1.288393 0.4878720 -2.640842 8.270020e-03 0.179783041
## Cd63     1858.8846      -1.229036 0.4046110 -3.037575 2.384899e-03 0.091726896
## Scimp    3214.2971      -1.178549 0.2970154 -3.967971 7.248715e-05 0.007659816
## Cdh9     2399.4879      -1.174131 0.3803598 -3.086895 2.022593e-03 0.089243134
## Cd2ap    5102.4494      -1.097587 0.4742872 -2.314182 2.065777e-02 0.264437984
## Synpo2   8661.0593       1.092095 0.5254055  2.078575 3.765646e-02 0.335192074
## Enpp2   49518.0321      -1.082679 0.4130321 -2.621295 8.759638e-03 0.182492463
## Nectin3  2785.1227      -1.081607 0.4692021 -2.305206 2.115504e-02 0.264437984
## Gpr63    3002.4449      -1.059907 0.3838702 -2.761108 5.760566e-03 0.151593838
## Gm14964  2786.5810      -1.015902 0.4583859 -2.216258 2.667384e-02 0.288920200

4.3.4 Front Cortex, nSD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue        padj
## Mapk1    3104.2402      -2.218915 0.5739169 -3.866264 1.105152e-04 0.013703883
## Tnik     1768.3125      -1.581507 0.5027979 -3.145413 1.658523e-03 0.061697060
## Rims1    6144.3140      -1.542799 0.3896719 -3.959225 7.519345e-05 0.013703883
## Crebbp   1779.6250      -1.529439 0.5165919 -2.960633 3.070074e-03 0.091815104
## Ddit4l    499.3928      -1.444243 0.4328069 -3.336923 8.471145e-04          NA
## Kcnh7    4004.9201      -1.272078 0.4412429 -2.882942 3.939801e-03 0.099172287
## Nectin3  1595.6233      -1.260374 0.4410248 -2.857831 4.265475e-03 0.099172287
## Nrn1     6211.3790      -1.232641 0.3700891 -3.330661 8.664010e-04 0.046043025
## Coch     1950.6947      -1.209003 0.3287500 -3.677575 2.354615e-04 0.021897923
## Npy1r    1832.5588      -1.207238 0.3483518 -3.465572 5.291049e-04 0.035665480
## Igf2     6235.0451      -1.179828 0.4825696 -2.444887 1.448977e-02 0.215607760
## Ngb      1200.2031       1.151301 0.5441568  2.115752 3.436591e-02          NA
## Enpp2   22600.8521      -1.148215 0.2619749 -4.382920 1.170991e-05 0.004356085
## Slc6a3   1125.7597       1.130957 0.5427395  2.083794 3.717890e-02          NA
## Neurod6  5231.8513      -1.079257 0.4712125 -2.290384 2.199909e-02 0.282195202
## Calb2    6249.1469       1.054973 0.5081247  2.076209 3.787461e-02 0.352233887
## Mas1     4070.1741      -1.046227 0.3550125 -2.947013 3.208592e-03 0.091815104

4.4 CA1 Glut

4.4.1 CA1, 4m, SD vs nSD

##      baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Fosb 65.82303        -1.2315 0.5028387 -2.449096 0.01432151 0.9998024

4.4.2 CA1, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Col6a1 46.47429      -1.099649 0.5210937 -2.110271 0.03483498 0.9981926

4.4.3 CA1, SD, 18m vs 4m

##            baseMean log2FoldChange     lfcSE      stat       pvalue
## Mapk1     152.56820      -3.060532 0.8974183 -3.410375 6.487372e-04
## Col6a1     75.84606       2.331295 0.5224536  4.462205 8.112053e-06
## Pten       44.49544      -1.832961 0.5045958 -3.632532 2.806535e-04
## Crebbp     61.76913      -1.659432 0.4804898 -3.453626 5.531029e-04
## Cd63       31.43783      -1.621291 0.5096757 -3.181025 1.467550e-03
## Rims1     112.71841      -1.610565 0.3295337 -4.887405 1.021736e-06
## Osr1       13.93035      -1.588537 0.6698127 -2.371614 1.771057e-02
## Scimp      68.04926      -1.570067 0.3590316 -4.373060 1.225171e-05
## Kcnh7     211.84604      -1.563109 0.4151966 -3.764743 1.667205e-04
## Aph1b      35.00426      -1.522892 0.5647031 -2.696801 7.000920e-03
## Gng2      147.05643      -1.452707 0.3047149 -4.767429 1.865913e-06
## Htr2c      12.58341      -1.410289 0.7140349 -1.975098 4.825706e-02
## Nrn1      247.86821      -1.393467 0.2670708 -5.217596 1.812600e-07
## Gabra1    447.43112      -1.382199 0.2992479 -4.618910 3.857613e-06
## Tgfbr1     12.03155      -1.363714 0.6638327 -2.054303 3.994634e-02
## Rgs5       20.29598      -1.345665 0.5288117 -2.544696 1.093730e-02
## Vip        22.45325      -1.313567 0.5571455 -2.357673 1.838986e-02
## Pthlh      92.33236       1.312689 0.4232590  3.101384 1.926185e-03
## Fam107a   202.83942      -1.278128 0.3466581 -3.687000 2.269134e-04
## Creb1      22.94129      -1.253724 0.5297952 -2.366432 1.796047e-02
## Mfsd2a     18.99395      -1.193663 0.5392621 -2.213513 2.686232e-02
## Cxcl10     28.87740       1.151695 0.4920407  2.340650 1.925021e-02
## Gpr63     239.21112      -1.132138 0.3694192 -3.064642 2.179305e-03
## Cd2ap      69.48275      -1.116352 0.4533377 -2.462518 1.379653e-02
## Fermt2    152.21579      -1.114068 0.3121525 -3.568985 3.583672e-04
## Rims2     213.95151      -1.100345 0.2967790 -3.707625 2.092119e-04
## Cd83       54.95034      -1.089725 0.4011008 -2.716836 6.590923e-03
## Enpp2     127.36040      -1.077678 0.3949238 -2.728825 6.356035e-03
## Cdh12      95.21613      -1.064576 0.3402567 -3.128745 1.755547e-03
## Gsto1      39.85407      -1.052179 0.4204573 -2.502464 1.233322e-02
## Lpl        29.81177      -1.046018 0.5176534 -2.020692 4.331162e-02
## Plp1      337.45238      -1.041314 0.2846385 -3.658374 2.538207e-04
## Serpina3n 157.09700      -1.014301 0.3173061 -3.196600 1.390575e-03
## Grm3       70.92527      -1.000590 0.3382539 -2.958103 3.095391e-03
##                   padj
## Mapk1     1.640378e-02
## Col6a1    5.743333e-04
## Pten      9.031941e-03
## Crebbp    1.506142e-02
## Cd63      2.980946e-02
## Rims1     1.808473e-04
## Osr1                NA
## Scimp     7.228506e-04
## Kcnh7     8.431293e-03
## Aph1b     6.044696e-02
## Gng2      2.201777e-04
## Htr2c               NA
## Nrn1      6.416603e-05
## Gabra1    3.413988e-04
## Tgfbr1              NA
## Rgs5                NA
## Vip                 NA
## Pthlh     3.099407e-02
## Fam107a   8.925259e-03
## Creb1               NA
## Mfsd2a              NA
## Cxcl10    1.329627e-01
## Gpr63     3.354234e-02
## Cd2ap     1.061733e-01
## Fermt2    1.057183e-02
## Rims2     8.925259e-03
## Cd83      5.832967e-02
## Enpp2     5.832967e-02
## Cdh12     3.011877e-02
## Gsto1     9.922635e-02
## Lpl       2.071934e-01
## Plp1      8.985254e-03
## Serpina3n 2.980946e-02
## Grm3      4.058523e-02

4.4.4 CA1, nSD, 18m vs 4m

##          baseMean log2FoldChange     lfcSE      stat       pvalue      padj
## Chrna6   19.67951       1.666178 0.4754129  3.504696 0.0004571284 0.2281071
## Nectin3  47.46258      -1.631437 0.5395209 -3.023863 0.0024956960 0.4151174
## Crebbp   55.58805      -1.392473 0.6546302 -2.127113 0.0334106741 0.9511837
## Rims1    96.25567      -1.178207 0.4683167 -2.515833 0.0118751318 0.8386956
## Fosb     80.55486       1.171907 0.5678902  2.063616 0.0390541737 0.9511837
## Col11a1 547.60932      -1.154765 0.3790488 -3.046482 0.0023153623 0.4151174
## Tnik     74.09373      -1.048673 0.5044715 -2.078755 0.0376398811 0.9511837
## Trem2    49.35988      -1.011562 0.4370855 -2.314335 0.0206493564 0.9511837

4.5 CA3 Glut

4.5.1 CA3, 4m, SD vs nSD

##       baseMean log2FoldChange     lfcSE     stat       pvalue        padj
## Calb2 29.82477       2.051544 0.4488261 4.570910 4.856107e-06 0.002428053
## Pomc  20.86806       1.612490 0.7007676 2.301034 2.138974e-02 0.999424500
## Lef1  21.37378       1.102830 0.5148673 2.141970 3.219591e-02 0.999424500

4.5.2 CA3, 4m, SD vs nSD

##     baseMean log2FoldChange   lfcSE      stat     pvalue     padj
## Agt 19.29474      -1.261918 0.54177 -2.329251 0.01984578 0.997665

4.5.3 CA3, SD, 18m vs 4m

##            baseMean log2FoldChange     lfcSE      stat       pvalue
## Mapk1      96.70723      -2.797088 0.9422508 -2.968518 2.992397e-03
## Nectin3    94.11829      -2.650630 0.9847415 -2.691701 7.108864e-03
## Fmo1       22.72425      -1.864992 0.7204081 -2.588799 9.631126e-03
## Rims1     125.30259      -1.804023 0.3509276 -5.140727 2.736775e-07
## Cdh9       80.74375      -1.710960 0.4120177 -4.152637 3.286652e-05
## Gpr63      54.51819      -1.681459 0.4957066 -3.392044 6.937330e-04
## Aph1b      12.14087      -1.608115 0.7086056 -2.269407 2.324357e-02
## Drd2       27.50701      -1.608077 0.5128373 -3.135647 1.714753e-03
## Sla        16.21457      -1.600248 0.7097770 -2.254578 2.415983e-02
## Nrn1      293.31061      -1.513779 0.3108338 -4.870058 1.115657e-06
## Cxcl10     17.83327       1.336723 0.5609055  2.383151 1.716515e-02
## Crebbp     38.56529      -1.304990 0.6297910 -2.072100 3.825613e-02
## Calb2      39.02454       1.284262 0.4614994  2.782804 5.389134e-03
## Cd2ap      45.94890      -1.275721 0.4892195 -2.607667 9.116165e-03
## Pten       32.75776      -1.267329 0.5498387 -2.304910 2.117159e-02
## Cdh12      45.33086      -1.250016 0.4222776 -2.960176 3.074635e-03
## Gsto1      24.06958      -1.222902 0.4947700 -2.471658 1.344883e-02
## Tlr4       24.76203      -1.212746 0.5234835 -2.316683 2.052099e-02
## Tnik       43.38206      -1.206358 0.4799521 -2.513496 1.195410e-02
## Klk6       27.27520       1.136663 0.4751948  2.391994 1.675711e-02
## Gng2      103.11553      -1.102622 0.3869352 -2.849630 4.377005e-03
## Neurod6   292.42755      -1.077181 0.3811013 -2.826496 4.706040e-03
## Serpina3n  70.41562      -1.074227 0.3552259 -3.024066 2.494016e-03
## Scimp      38.01897      -1.072117 0.4720622 -2.271136 2.313874e-02
## Cldn5     130.71945       1.055569 0.4638584  2.275628 2.286828e-02
## Fermt2     91.57595      -1.030736 0.3421934 -3.012146 2.594079e-03
## Bace1      49.40905      -1.007580 0.3874615 -2.600466 9.309731e-03
##                   padj
## Mapk1     0.0784031910
## Nectin3   0.0939642951
## Fmo1      0.0991256923
## Rims1     0.0000837453
## Cdh9      0.0033523850
## Gpr63     0.0424564579
## Aph1b               NA
## Drd2      0.0720600640
## Sla                 NA
## Nrn1      0.0001706954
## Cxcl10              NA
## Crebbp    0.2053750320
## Calb2     0.0884158530
## Cd2ap     0.0991256923
## Pten      0.1439668309
## Cdh12     0.0784031910
## Gsto1     0.1228233021
## Tlr4      0.1439668309
## Tnik      0.1179985350
## Klk6      0.1349388655
## Gng2      0.0884158530
## Neurod6   0.0884158530
## Serpina3n 0.0784031910
## Scimp     0.1475094521
## Cldn5     0.1475094521
## Fermt2    0.0784031910
## Bace1     0.0991256923

4.5.4 CA3, nSD, 18m vs 4m

##          baseMean log2FoldChange     lfcSE      stat       pvalue       padj
## Rims1   122.02774      -1.759470 0.4511505 -3.899963 0.0000962075 0.04810375
## Crebbp   32.82484      -1.717662 0.5431351 -3.162494 0.0015642387 0.26070645
## Rspo1    12.52315      -1.513906 0.6752653 -2.241943 0.0249650722 0.86205315
## Col6a1   74.09823       1.377491 0.4636508  2.970965 0.0029686518 0.37108148
## Synpr    17.53155      -1.253856 0.5627003 -2.228284 0.0258615946 0.86205315
## Tnik     49.15606      -1.228526 0.5329225 -2.305262 0.0211518791 0.86205315
## Htr1a    29.52066      -1.138947 0.4513009 -2.523699 0.0116127426 0.82948161
## Hsd11b1  20.24491      -1.112675 0.5402333 -2.059620 0.0394348615 0.93131111
## Gpr37    37.90748      -1.046958 0.4130462 -2.534725 0.0112535789 0.82948161
## Rims2   134.37693      -1.023151 0.3117266 -3.282205 0.0010299856 0.25749640

4.6 DG Glut

4.6.1 DG, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Cd4    1.441795       4.001266 1.9877728  2.012940 0.04412099 0.9997526
## Cux2   1.615010      -3.987675 1.8577386 -2.146521 0.03183143 0.9997526
## Nnat   6.838911      -1.729596 0.8614498 -2.007773 0.04466741 0.9997526
## Nr4a1 12.890494      -1.368803 0.6770528 -2.021708 0.04320652 0.9997526
## Egr1  27.310567      -1.153685 0.5041164 -2.288528 0.02210677 0.9997526

4.6.2 DG, 4m, SD vs nSD

## [1] baseMean       log2FoldChange lfcSE          stat           pvalue        
## [6] padj          
## <0 rows> (or 0-length row.names)

4.6.3 DG, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Creb1     8.838619      -3.540733 1.4029857 -2.523713 1.161227e-02           NA
## Osr1      4.312403      -3.531686 1.6380477 -2.156033 3.108106e-02           NA
## Mapk1   110.720229      -3.151802 1.1344168 -2.778345 5.463653e-03 0.0761206451
## Sulf2     6.545435      -2.934066 1.4668794 -2.000209 4.547769e-02           NA
## Pcdh11x  10.087379      -2.799634 1.2592253 -2.223299 2.619567e-02           NA
## Pten     27.204742      -2.280146 0.7753240 -2.940895 3.272656e-03 0.0617635780
## Igfbp6   13.685701      -2.166661 1.0276651 -2.108334 3.500212e-02           NA
## Batf3    13.905444      -2.061392 0.9783259 -2.107061 3.511229e-02           NA
## Drd2     15.229984      -1.978422 0.9188411 -2.153171 3.130526e-02           NA
## Npy1r    89.088059      -1.927346 0.4749452 -4.058040 4.948637e-05 0.0026833698
## Trib2    23.553423      -1.901210 0.7251365 -2.621866 8.744991e-03 0.0870524059
## Mfsd2a   23.696306      -1.843867 0.7014478 -2.628659 8.572227e-03 0.0870524059
## Rims1    87.128681      -1.674065 0.4453630 -3.758878 1.706769e-04 0.0053397478
## Crebbp   34.223984      -1.649559 0.6771776 -2.435933 1.485344e-02 0.1121690729
## Cp       21.131692      -1.642743 0.7288942 -2.253746 2.421214e-02           NA
## Nnat     23.658280      -1.588440 0.6832939 -2.324680 2.008906e-02 0.1293971759
## Adarb2   54.166987      -1.536173 0.5808529 -2.644686 8.176684e-03 0.0870524059
## Dkk3    120.215937       1.519698 0.3053695  4.976587 6.471515e-07 0.0001417262
## Nrn1    275.875815      -1.448143 0.3195334 -4.532055 5.841266e-06 0.0006396187
## Gabra1  140.589194      -1.442634 0.3599486 -4.007888 6.126415e-05 0.0026833698
## Cdh12    49.337250      -1.342794 0.4856149 -2.765142 5.689808e-03 0.0761206451
## Hs3st1   32.842991      -1.281491 0.5745614 -2.230382 2.572211e-02 0.1482406001
## Kctd4   229.707578      -1.247941 0.2864377 -4.356763 1.319999e-05 0.0009635994
## Bace1    49.699778      -1.239075 0.4955976 -2.500163 1.241361e-02 0.0970921578
## Gng2    114.342153      -1.208708 0.4193616 -2.882259 3.948357e-03 0.0617635780
## Ccl6     36.457623       1.102447 0.4892745  2.253229 2.424472e-02 0.1435025600
## Fermt2   78.033576      -1.099614 0.4320875 -2.544888 1.093129e-02 0.0970921578
## Rims2    81.157211      -1.028183 0.4096605 -2.509841 1.207855e-02 0.0970921578
## Prox1   308.020078      -1.002059 0.2626136 -3.815716 1.357886e-04 0.0049562837

4.6.4 DG, nSD, 18m vs 4m

##        baseMean log2FoldChange     lfcSE      stat       pvalue      padj
## Mapk1  61.53882      -2.648736 1.1590254 -2.285313 0.0222944657 0.9987521
## Rims1  63.32509      -1.563496 0.4604135 -3.395851 0.0006841558 0.3420779
## Adarb2 28.93418      -1.346367 0.6409590 -2.100551 0.0356804424 0.9987521
## Gng2   75.69529      -1.217834 0.4313223 -2.823489 0.0047503990 0.7103968
## Dkk3   81.20299       1.104258 0.3483491  3.169974 0.0015245266 0.3811316
## Nos1   40.84720      -1.086536 0.4572932 -2.376015 0.0175007333 0.9722630

4.7 Microglia

4.7.1 Microglia, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Pilra  8.356982      -1.484263 0.7027468 -2.112088 0.03467892 0.9991502
## Nts    9.439281      -1.393225 0.6952182 -2.004011 0.04506883 0.9991502
## Kcnq1 27.739852      -1.285856 0.6186094 -2.078624 0.03765196 0.9991502

4.7.2 Microglia, 4m, SD vs nSD

##         baseMean log2FoldChange     lfcSE      stat     pvalue      padj
## Cxcl10  14.04880      -1.450298 0.7294729 -1.988145 0.04679569 0.9989715
## Ccdc153 19.29723      -1.210721 0.6141815 -1.971275 0.04869244 0.9989715

4.7.3 Microglia, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Cxcl10    34.43829       3.185087 1.2507666  2.546508 1.088068e-02 1.308472e-01
## Ube3a    183.87194       3.032369 0.4585702  6.612659 3.774779e-11 1.770371e-08
## Mapk1     97.52984      -2.024096 0.8614472 -2.349646 1.879129e-02 1.728062e-01
## Pten     100.80738      -1.860455 0.5094786 -3.651685 2.605254e-04 1.018220e-02
## Gpr17    161.77838      -1.761952 0.3951373 -4.459087 8.230934e-06 6.433847e-04
## Lgals3    45.38724       1.741305 0.3973101  4.382735 1.171987e-05 7.852310e-04
## Ly9      553.75907       1.595102 0.2655153  6.007569 1.883252e-09 4.416226e-07
## Bace1     25.07478      -1.531592 0.5023875 -3.048626 2.298905e-03 4.538742e-02
## Nrn1      58.03720      -1.511798 0.4188369 -3.609514 3.067708e-04 1.106735e-02
## Rims1    113.85149      -1.458970 0.3577024 -4.078725 4.528343e-05 2.123793e-03
## Krt73     92.35455       1.404952 0.2944249  4.771852 1.825392e-06 2.853696e-04
## C4b       97.98965       1.344343 0.3257714  4.126645 3.680944e-05 1.918181e-03
## Crebbp    49.34710      -1.287271 0.5759229 -2.235144 2.540789e-02 2.248359e-01
## Car4      47.20873      -1.250344 0.3784741 -3.303646 9.543617e-04 2.237978e-02
## Jam2     129.66134      -1.232333 0.3609923 -3.413739 6.407798e-04 1.760904e-02
## Cst7      36.36832       1.149199 0.4001300  2.872065 4.077996e-03 6.595104e-02
## Gfap     707.23835       1.063775 0.2455991  4.331347 1.481997e-05 8.688205e-04
## Csf1     407.35253       1.061309 0.2960703  3.584653 3.375266e-04 1.130714e-02
## Cx3cr1 14167.31892      -1.051905 0.2289954 -4.593565 4.357368e-06 5.109014e-04
## Tacr2     32.85523      -1.039224 0.4183249 -2.484250 1.298247e-02 1.449710e-01
## Gng2     270.75816      -1.025675 0.3080212 -3.329885 8.688199e-04 2.144613e-02
## P2ry12  3897.50513      -1.009820 0.3126185 -3.230200 1.237035e-03 2.762711e-02
## Prkce    177.03247      -1.008273 0.3844606 -2.622565 8.727052e-03 1.106213e-01
## Hs3st1   100.65168       1.000271 0.3632286  2.753833 5.890180e-03 8.632795e-02
## Chrna7    26.53656      -1.000061 0.5010288 -1.996014 4.593235e-02 3.205807e-01

4.7.4 Microglia, nSD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Ube3a    181.80186       3.041205 0.8960115  3.394159 6.883975e-04 1.351433e-02
## Mapk1     98.01886      -2.237669 0.5837262 -3.833422 1.263730e-04 3.625933e-03
## Lgals3    46.94724       1.781549 0.3610819  4.933918 8.059622e-07 1.002080e-04
## Ly9      639.09507       1.706257 0.1836924  9.288664 1.562367e-20 5.827628e-18
## Hs3st1    99.30783       1.539458 0.3805613  4.045230 5.227173e-05 2.166373e-03
## Prkce    180.71848      -1.509355 0.4519899 -3.339354 8.397334e-04 1.430500e-02
## Pten      98.23140      -1.478363 0.4949702 -2.986771 2.819410e-03 2.921222e-02
## Crebbp    57.62455      -1.472084 0.5195135 -2.833582 4.602955e-03 4.187567e-02
## Trhr      20.56049       1.405772 0.7167553  1.961300 4.984403e-02           NA
## Clec7a    48.15243       1.402349 0.3606876  3.887990 1.010779e-04 3.141839e-03
## Cd74     270.68265       1.359913 0.2938595  4.627767 3.696300e-06 2.757439e-04
## Gfap     731.29154       1.338545 0.2611368  5.125839 2.962161e-07 5.524431e-05
## Cxcr4     16.19788       1.319395 0.5787165  2.279864 2.261578e-02           NA
## Krt73     94.17857       1.303918 0.3043821  4.283821 1.837106e-05 9.789152e-04
## Car4      40.78166      -1.226681 0.4072136 -3.012376 2.592113e-03 2.762452e-02
## Cd2ap    232.74810      -1.213374 0.4297161 -2.823664 4.747814e-03 4.216511e-02
## Rims1     94.71936      -1.206083 0.3639595 -3.313783 9.204293e-04 1.430500e-02
## Pkp2      24.85369       1.205030 0.4868917  2.474946 1.332564e-02           NA
## Itgal     49.52770       1.192854 0.3593647  3.319341 9.023010e-04 1.430500e-02
## Cst7      51.11475       1.175153 0.3527500  3.331404 8.640904e-04 1.430500e-02
## Jam2     141.84737      -1.149856 0.3664407 -3.137904 1.701606e-03 2.115663e-02
## Csf1     459.62288       1.128637 0.2757863  4.092432 4.268722e-05 1.990292e-03
## Pdlim5   106.46560      -1.127467 0.3854098 -2.925371 3.440457e-03 3.290488e-02
## P2ry12  3928.08674      -1.101162 0.3413644 -3.225767 1.256356e-03 1.673645e-02
## Apoe   10100.52400       1.099799 0.2420314  4.544033 5.518791e-06 3.430848e-04
## C3        59.54743       1.080231 0.4888754  2.209624 2.713126e-02 1.556917e-01
## Cx3cr1 14371.50486      -1.069597 0.2214226 -4.830568 1.361442e-06 1.269545e-04
## Ccl6      79.96391      -1.034753 0.4369001 -2.368398 1.786531e-02 1.170984e-01
## Grin3a    33.37285      -1.032305 0.4768214 -2.164973 3.038975e-02 1.691847e-01
## Casp8    545.41043      -1.003078 0.3182875 -3.151485 1.624424e-03 2.089345e-02

4.8 Astrocyte

4.8.1 Astrocyte, 4m, SD vs nSD

## [1] baseMean       log2FoldChange lfcSE          stat           pvalue        
## [6] padj          
## <0 rows> (or 0-length row.names)

4.8.2 Astrocyte, 4m, SD vs nSD

##        baseMean log2FoldChange     lfcSE     stat      pvalue      padj
## Cxcl10 177.1741      -1.892756 0.6142599 -3.08136 0.002060574 0.9995905

4.8.3 Astrocyte, SD, 18m vs 4m

##           baseMean log2FoldChange     lfcSE      stat       pvalue         padj
## Cxcl10   219.02254       2.523149 0.5368487  4.699926 2.602553e-06 5.868758e-04
## Mapk1    733.82523      -2.159191 0.8969952 -2.407138 1.607810e-02 1.154801e-01
## Tnik     390.52383      -1.871317 0.4757218 -3.933637 8.366996e-05 5.390736e-03
## Aph1b    252.89006      -1.833210 0.4605169 -3.980766 6.869365e-05 5.390736e-03
## Pten     454.36091      -1.658461 0.4715872 -3.516764 4.368418e-04 1.393180e-02
## Ddit4l   325.01639      -1.588108 0.4543943 -3.495000 4.740614e-04 1.393180e-02
## Scimp    360.85337      -1.545617 0.2942883 -5.252051 1.504147e-07 6.783701e-05
## Fmo1     865.95003      -1.531348 0.4306553 -3.555856 3.767504e-04 1.393180e-02
## Clic6   1573.12697       1.463319 0.3598292  4.066703 4.768294e-05 5.376252e-03
## Crebbp   479.33902      -1.338766 0.4579029 -2.923689 3.459098e-03 4.588392e-02
## Gm14964 2112.37766      -1.253496 0.3355748 -3.735369 1.874404e-04 1.056695e-02
## Htr2c    146.94141      -1.239408 0.4578314 -2.707128 6.786812e-03 6.935394e-02
## Rims1    598.49478      -1.194565 0.3021002 -3.954200 7.679123e-05 5.390736e-03
## Tshr     100.83117      -1.191223 0.4239309 -2.809946 4.954985e-03           NA
## Synpr     78.66474      -1.175632 0.5228535 -2.248493 2.454479e-02           NA
## Mhrt     192.35960      -1.162943 0.3941672 -2.950380 3.173838e-03 4.588392e-02
## Cd63     758.06994      -1.101061 0.4108220 -2.680140 7.359130e-03 6.935394e-02
## Npy2r    231.55009      -1.098837 0.3597531 -3.054419 2.254965e-03 4.078358e-02
## Ube3a    285.65333       1.074286 0.3083617  3.483851 4.942544e-04 1.393180e-02
## Cd2ap    960.31017      -1.061344 0.4242341 -2.501789 1.235677e-02 9.894220e-02
## Grin3a  1637.97798      -1.050680 0.3209665 -3.273489 1.062286e-03 2.395455e-02
## Atp13a5 2455.37536      -1.021468 0.2857244 -3.575012 3.502121e-04 1.393180e-02
## Gng2     448.01979      -1.020429 0.3314888 -3.078321 2.081705e-03 4.078358e-02
## Bace1    809.58118      -1.019204 0.2445438 -4.167778 3.075834e-05 4.624004e-03
## Jam2    2444.87768      -1.008393 0.3065624 -3.289356 1.004170e-03 2.395455e-02

4.8.4 Astrocyte, nSD, 18m vs 4m

##          baseMean log2FoldChange     lfcSE      stat       pvalue      padj
## Chrna6   19.67951       1.666178 0.4754129  3.504696 0.0004571284 0.2281071
## Nectin3  47.46258      -1.631437 0.5395209 -3.023863 0.0024956960 0.4151174
## Crebbp   55.58805      -1.392473 0.6546302 -2.127113 0.0334106741 0.9511837
## Rims1    96.25567      -1.178207 0.4683167 -2.515833 0.0118751318 0.8386956
## Fosb     80.55486       1.171907 0.5678902  2.063616 0.0390541737 0.9511837
## Col11a1 547.60932      -1.154765 0.3790488 -3.046482 0.0023153623 0.4151174
## Tnik     74.09373      -1.048673 0.5044715 -2.078755 0.0376398811 0.9511837
## Trem2    49.35988      -1.011562 0.4370855 -2.314335 0.0206493564 0.9511837

4.9 DE frequency table

Regulation Gene Freq in DE above
	Gene	Freq
131	Rims1	14
41	Crebbp	13
95	Mapk1	11
110	Nrn1	8
128	Pten	8
153	Tnik	8
46	Cxcl10	7
69	Gng2	7
101	Nectin3	7
20	Cd2ap	6
6	Aph1b	5
9	Bace1	5
13	Calb2	5
37	Col6a1	5
58	Enpp2	5
80	Htr2c	5
134	Scimp	5
144	Synpr	5
22	Cd63	4
34	Clic6	4
65	Fosb	4
85	Kcnh7	4
107	Npy1r	4
151	Th	4
3	Adarb2	3
17	Ccdc153	3
26	Cdh12	3
27	Cdh9	3
35	Coch	3
36	Col11a1	3
40	Creb1	3
50	Ddit4l	3
55	Drd2	3
61	Fermt2	3
63	Fmo1	3
64	Folr1	3
68	Gm14964	3
71	Gpr37	3
72	Gpr63	3
74	Grin3a	3
77	Hs3st1	3
84	Jam2	3
96	Mas1	3
119	Pdyn	3
120	Penk	3
132	Rims2	3
137	Six3	3
139	Slc6a3	3
143	Synpo2	3
158	Ube3a	3
4	Adora2a	2
5	Agt	2
11	C3	2
14	Car12	2
15	Car4	2
18	Ccl6	2
29	Chrna6	2
42	Csf1	2
43	Cst7	2
45	Cx3cr1	2
48	Dclk3	2
51	Dkk3	2
52	Dlk1	2
53	Dlx2	2
54	Drd1	2
62	Fibcd1	2
66	Gabra1	2
67	Gfap	2
76	Gsto1	2
81	Igf2	2
87	Kctd4	2
89	Krt73	2
91	Lgals3	2
94	Ly9	2
98	Mfsd2a	2
102	Neurod6	2
103	Ngb	2
104	Nnat	2
115	Osr1	2
116	P2ry12	2
125	Ppp1r1b	2
126	Prkce	2
136	Serpina3n	2
146	Tac1	2
154	Trem2	2
1	Ace	1
2	Acta2	1
7	Apoe	1
8	Atp13a5	1
10	Batf3	1
12	C4b	1
16	Casp8	1
19	Ccn2	1
21	Cd4	1
23	Cd74	1
24	Cd83	1
25	Cd9	1
28	Chrm4	1
30	Chrna7	1
31	Cldn11	1
32	Cldn5	1
33	Clec7a	1
38	Cp	1
39	Cpne5	1
44	Cux2	1
47	Cxcr4	1
49	Dcn	1
56	Egr1	1
57	Egr4	1
59	Enpp6	1
60	Fam107a	1
70	Gpr17	1
73	Gpr83	1
75	Grm3	1
78	Hsd11b1	1
79	Htr1a	1
82	Igfbp6	1
83	Itgal	1
86	Kcnq1	1
88	Klk6	1
90	Lef1	1
92	Lhx6	1
93	Lpl	1
97	Meis2	1
99	Mhrt	1
100	Mog	1
105	Nos1	1
106	Npas1	1
108	Npy2r	1
109	Nr4a1	1
111	Ntng1	1
112	Nts	1
113	Nxph4	1
114	Opalin	1
117	Pcdh11x	1
118	Pdlim5	1
121	Pilra	1
122	Pkp2	1
123	Plp1	1
124	Pomc	1
127	Prox1	1
129	Pthlh	1
130	Rgs5	1
133	Rspo1	1
135	Scn4b	1
138	Sla	1
140	Sncg	1
141	Sulf2	1
142	Syndig1l	1
145	Syt6	1
147	Tacr2	1
148	Tacr3	1
149	Tcf7l2	1
150	Tgfbr1	1
152	Tlr4	1
155	Trhr	1
156	Trib2	1
157	Tshr	1
159	Vip	1

Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic

ADP, anterodorsal preoptic nucleus

AHN, anterior hypothalamic nucleus

ARH, arcuate hypothalamic nucleus

CLI, central linear nucleus raphe

CUN, cuneiform nucleus

DMH, dorsomedial nucleus of the hypothalamus

DMX, dorsal motor nucleus of the vagus nerve

IF, interfascicular nucleus raphe

LHA, lateral hypothalamic area

MDRN, medullary reticular nucleus

MPN, medial preoptic nucleus

MPO, medial preoptic area

MV, medial vestibular nucleus

NTS, nucleus of the solitary tract

PAG, periaqueductal grey

PARN, parvicellular reticular nucleus

PB, parabrachial nucleus

PBG, parabigeminal nucleus

PGRN, paragigantocellular reticular nucleus

PGRNd, paragigantocellular reticular nucleus, dorsal part

PH, posterior hypothalamic nucleus

PMv, ventral premammillary nucleus

PPN, pedunculopontine nucleus

PVa, periventricular hypothalamic nucleus, anterior part

PVHd, paraventricular hypothalamic nucleus, descending division

PVi, periventricular hypothalamic nucleus, intermediate part

PVpo, periventricular hypothalamic nucleus, preoptic part

PVR, periventricular region

RAmb, midbrain raphe nuclei

RL, rostral linear nucleus raphe

SBPV, subparaventricular zone

SNc, substantia nigra, compact part

SPIV, spinal vestibular nucleus

TMv, tuberomammillary nucleus, ventral part

VII, facial motor nucleus

VMPO, ventromedial preoptic nucleus

VTA, ventral tegmental area

ZI, zona incerta.